Molecular Models of Rosmarinic Acid and DPPHWilliam F. ColemanThe paper by Canelas and da Costa (1) introduces students to the antioxidant rosmarinic acid, and its interaction with the free radical DPPH. Those two molecules are the featured species this month. The original paper shows the 2-dimensional structure of the cis isomer of rosmarinic acid, although the trans isomer exhibits very similar antioxidant properties. Calculations at the DFT/B3LYP 631-G(d) level show that the trans isomer is more stable than the cis isomer in the gas phase, a situation that is expected to carry over into solution. Many antioxidants are phenols, and rosmarinic acid has four such groups available for radical formation. A DFT study by Cao et al. (2) examines the relative stabilities of the radicals formed from loss of each of the phenolic hydrogens. That paper focuses on the trans isomer, and a useful student project would be to repeat the calculations with the cis isomer. An HPLC separation of the isomers of rosmarinic acid has been published (3), and might well lead to an extension of the experiment described in ref 1 in which relative antioxidant efficiencies of the two isomers could be evaluated. DPPH has been used extensively as a standard for determining antioxidant activity. An examination of the molecular orbital occupied by the lone electron shows significant delocalization, providing a partial explanation for the stability of the neutral radical. Our gas phase structure for DPPH, also at the DFT/B3LYP 631-G(d) level, is quite consistent with several crystal structures on DPPH and DPPH in the presence of another species (4).

Molecular Models of ResveratrolWilliam F. ColemanThe featured molecules this month are from the paper "Resveratrol Photoisomerization: An Integrative Guided-Inquiry Experiment" by Bernard, Gernigon, and Britz-McKibbin exploring trans to cis photoisomerization in resveratrol. Examination of Figure 1 in that paper, where the hydrogen atoms have been omitted, might lead one to conclude that the structures are relatively straightforward. These isomers provide students an excellent opportunity to test their ability to take a two-dimensional representation and envision the three-dimensional structure of the molecule and to consider the competing factors that might lead to the three-dimensional structures being non-planar. The two-dimensional models focus attention on the possibility of extended pi-electron delocalization. Addition of the hydrogen atoms clearly suggests that delocalization will compete with non-bonded H-H repulsions in the cis isomer. Further examination of the trans isomer shows that such non-bonded interactions are, in what one might call a first-order approximation, like those in biphenyl interactions that lead biphenyl to be non-planar in both the gas phase and in a variety of solvents. The backbone of the trans isomer of resveratrol, trans-stilbene, has been the subject of a number of theoretical and experimental investigations (1, 2). In general, Hartree-Fock calculations predict a non-planar geometry for this molecule while Density Functional Calculations, using the same basis sets, predict an essentially planar structure. Spectroscopic evidence supports a temperature-dependent structure for trans-stilbene with the molecule being planar at low temperature and non-planar at high temperatures. Our calculations on trans-resveratrol produce similar results. Hartree-Fock calculations using the 6-31G** (6- 31G(d,p)) basis set predict a dihedral angle of approximately 24 degrees between each ring and the central carbon-carbon double bond. This result is consistent with the reported value of 23 degrees using the 6-31G* basis set. We also find that DFT calculations using the B3LYP functional and the 6- 31G** basis set, lead to a planar configuration. We include several versions of trans-stilbene and trans-resveratrol in the molecule collection so that students can explore these structural questions in more detail. For each molecule, structures obtained from PM3, HF(6-31G**), and DFT(B3LYP/6-31G**) calculations are included, as well as planar and non-planar structures of biphenyl. Measurement of the various bond and torsion angles using Jmol will help students develop a sense of the distance dependence of the non-bonded interactions and their importance in determining the actual structure. They might also wish to consider what additional degree(s) of freedom resveratrol and stilbene have that biphenyl does not, allowing the trans-form of the former molecules to remain planar under certain conditions, while minimizing the effect of the non-bonded repulsions.

Plant Chemistry |

Natural Products

Molecular Models of Antioxidants and RadicalsWilliam F. ColemanThis month's featured molecules come from the paper by John M. Berger, Roshniben J. Rana, Hira Javeed, Iqra Javeed, and Sandi L. Schulien (1) describing the use of DPPH to measure antioxidant activity. DPPH was one of the featured molecules in September 2007 (2) and the basics of antioxidant activity were introduced in last month's column (3). In addition, some of the other molecules in the paper are already in the featured molecules collection (4). The remaining structures in the Figure 1 and Table 1 of the paper have been added to the collection. All structures have been optimized at the 6-311G(D,P) level. These molecules suggest a number of possible student activities, some reminiscent of previous columns and some new. (R,R,R)-α-tocopherol is one of the molecules in the mixture that goes by the name vitamin E. These molecules differ in the substituents on the benzene ring and on whether or not there are alternating double bonds in the phytyl tail. In (R,R,R)-α-tocopherol the R's refer to the three chiral carbon atoms in tail while α refers to the substituents on the ring. (R,R,R)-α-Tocopherol is the form found in nature. An interesting literature problem would be to have students learn more about the vitamin E mixture and the differing antioxidant activity of the various constituents. Additionally they could be asked to explore the difference between the word natural as used by a chemist, and "natural" as used on vitamin E supplements. Can students find regulations governing the use of the term "natural"? Can they suggest alternative legislation, and defend their ideas? If students read about vitamin C they will discover that only L-ascorbic acid is useful in the body. It would be interesting to extend the experiment described in the Berger et al. paper (1) to include D-ascorbic acid. How do the antioxidant abilities of the enantiomers, as determined by reaction with DPPH compare? Is this consistent with the behavior in the body? Why or why not? Berger et al. mention two other stable neutral radicals, TEMPO (2,2,6,6-tetramethylpiperidine-1-oxyl) and Fremy's salt. In a reversal from the use of stable radicals to measure antioxidant properties, these two molecules have proven to be very versatile oxidation catalysts in organic synthesis, and would make a rich source of research papers for students in undergraduate organic courses.

Free Radicals |

Natural Products

Molecular Models of Lycopene and Other CarotenoidsWilliam F. ColemanOver the past decade or so the phrase emerging research suggests has entered the argot of advertising, and that phrase has been applied to this month's Featured Molecule, lycopene, particularly with regard to potential health benefits of tomatoes. The paper by Jie Zhu, Mingjie Zhang, and Qingwei Liu (1) describes an extraction and purification of lycopene from tomato paste using an emulsion rather than the traditional solvent-based extraction. Lycopene is a member of the family of molecules called carotenoids, the most familiar of which is beta-carotene. This family of natural products includes more than 500 members that have been isolated and whose structures have been determined. Professor Hanspeter Pfander's research group at the University of Bern maintains a Web site with a significant amount of information on carotenoid structure, synthesis, and activity (2). Structurally one can think of carotenoids as consisting of three segments, a relatively rigid conjugated central portion with end groups. The end groups are, in general, flexible with respect to rotation about the bond connecting them to the central portion. For example, in beta-carotene, the dependence of total energy on the dihedral angle shown in Figure 1, displays a very broad range of essentially isoenergetic conformations (Figure 2). The energies shown in Figure 2 were calculated at the PM3 level using Hyperchem 7.5 (3). Calculations at the HF/631-G(d,p) level, with many fewer data points, show a similar trend. Many of the health benefits derived from various carotenoids are attributed to their antioxidant activities. Carotenoids react with singlet-oxygen in a physical, diffusion-controlled, quenching process that results in ground state triplet-oxygen and, following a non-radiative relaxation, ground state carotenoid. Of the various carotenoids that have been studied, lycopene and beta-carotene show the greatest quenching rate constants (4). The carotenoids provide us with countless explorations by students and teachers looking for connections between fundamental chemical concepts and real-world applications. Structure, reactivity, chemical synthesis, biosynthesis, and stereochemistry are just a few of the concepts involved in understanding the manifest important roles that these molecules play.

Plant Chemistry |

Natural Products

Molecular Models of Annatto Seed ComponentsWilliam F. ColemanIn January 2008 the focus of this column was on the plant pigments lycopene and beta-carotene (1). Our attention this month returns to two papers discussing the pigments in annatto seeds (Figure 1), including direct precursors to lycopene. The paper by Teixeira, Durï¿½n, and Guterres describes the extraction and encapsulation of annatto seed components (2). The McCullagh and Ramos paper describes the separation of the pigment bixin from these seeds by TLC and column chromatography (3). These molecules could form the basis of interesting exercises across the chemistry curriculum. In courses designed for non-majors, students could choose a molecule from the table and search the literature for both scientific and non-scientific sources. Are the claims made in the latter sources regarding the health benefits of these molecules consistent with the scientific data? That discussion could be expanded to the more general question of how one tests the validity of statements made in what are essentially advertisements. Are any of these precursor molecules to lycopene considered to have anticancer properties (4)? In introductory or general chemistry courses, students could explore the various bond lengths and bond angles in the molecules to see whether they are consistent with their expectations based on simple bonding models. In introductory, organic, or biochemistry classes, the thermodynamics of hydrogenation and dehydrogenation could be examined. This might make an interesting alternative to the oft-discussed Haber Process. What conditions would one propose for a dehydrogenation process? Why are dehydrogenation reactions important? What enzymes catalyze the various dehydrogenation steps from phytoene to lycopene? These molecules could also be used in a variety of computational exercises in introductory and physical chemistry courses. Hartreeï¿½Fock calculations on a molecule such as phytoene may prove time-consuming depending on the nature of the computing system available. A good place to begin would be to perform semi-empirical calculations on the various molecules. Do the optimized structures match experimental results or the results of larger calculations? Does the HOMOï¿½LUMO gap correlate with the observed electronic absorption spectra? Which is more important in determining the difference in absorption between phytoene and phytofluene, the total number of double bonds or the number of bonds in the region of conjugation? Of course the aspect of these molecules that is most likely to capture student attention is their color, and they provide nice examples of the origin of color, the relationship between color observed and color absorbed, and, in upper level courses, the more detailed relationships of the energies of the ground and excited states.

Molecular Model of ZinconWilliam F. ColemanThe Featured Molecules this month are the tautomeric forms of the colorimetric reagent zincon, used in the paper by Maria Mar Areco, Maria dos Santos Afonso, and Erika Valdman on the bioabsorption of zinc, and by extension other metal ions, by seaweed. The structures presented have been calculated at the DFT/6-31G(d) level using the B3LYP functional. These structures represent energy minima, but not necessarily global minima. The structures could be used as an introduction to the concept of tautomerism, with students being asked to develop a definition of the term based on their observations of the difference(s) in linkage in the two forms. An intramolecular hydrogen bond is found in each structure, and introductory chemistry students could be encouraged to look for these structural features in molecules that are more complex than those typically encountered to introduce hydrogen bonding. More advanced students could use computational techniques to explore the energy differences between the two forms, and compare those differences to the ones observed between more traditional keto/enol examples.

Calorimetry / Thermochemistry |

Water / Water Chemistry |

Biological Cells

Molecular Models of Plant HormonesWilliam F. ColemanThe paper "Synthesis of Plant Auxin Derivatives and Their Effects on Ceratopteris richardii" by Corey E. Stilts and Roxanne Fisher describing an experiment begun in the organic labs and completed in a biochemistry cell biology lab provides the featured molecules for this month. The molecules in Figure 1 of that paper have been added to the collection. There is nothing particularly surprising about their structures, but students might be interested in seeing whether they can determine any structure/regulating effect relationships as the number of synthesized auxin derivatives grows. Additionally, students with little or no biochemistry background might wish to explore other systems that act as growth regulating hormones in plants, as an introduction to the variety of molecular structures that can display such bioactivity. Such molecules range from the very simple, ethene, to the adenine-derived cytokinins (an example of which, zealtin, is shown here) and the brassinosteroids. Brassinolide, a commonly occurring brassin, is also shown. These latter two structures have also been added to the molecule collection. All of the structures have been optimized at the HF/6-31G(d) level.